Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights.
Tandem repeat (TR) expansions, including short TRs (motifs ≤6 bp) and variable number TRs (motifs >6 bp), underlie many monogenic disorders, with variable length and sequence influencing pathogenicity, penetrance, severity, and onset. Accurate genotype-phenotype correlation and disease prevalence estimation require characterization beyond repeat length. Here we present a population-scale analysis of 66 disease-associated TR loci using long-read assemblies from 2530 diverse haplotypes from 1265 unaffected donors. Integrating repeat length, motif composition, local ancestry, linkage disequilibrium, and phylogenetic analyses, we reveal extensive locus-, population-, and allele-specific variation shaping disease risk. Up to 8.5% of individuals carry expansions above established pathogenic thresholds, many containing interrupting motifs or sequence structures that attenuate pathogenicity. After excluding alleles from loci with uncertain disease association, non-pathogenic interrupted expansions, and carrier states inconsistent with inheritance patterns, ~4% carried expansions predicted to confer disease risk, largely at adult-onset loci with reduced penetrance. Ancestry-resolved analyses uncover population-specific TR architectures contributing to epidemiological disparities in repeat expansion disorders. Phylogenetic analyses identify conserved ancestral alleles and loci with recent instability. We describe variable linkage disequilibrium patterns and recombination signatures around specific disease-associated TR loci. Our findings emphasize integrating sequence, ancestry, and evolutionary context to understand the complex landscape of disease-associated TRs.